Pharma Computational Chemist

Cogent Scientific; San Diego (CA); On-site; USD 150,000 - 210,000; Full time

Job summary

Cogent Scientific is seeking a highly skilled Pharma Computational Chemist to lead analysis of protein structures for small-molecule discovery. You will integrate X-ray, cryo-EM, and predicted structures with biophysical data, using Schrödinger and other platforms to guide docking, screening, MD, and free-energy calculations.

The role emphasizes developing testable binding hypotheses, collaborating with medicinal chemists, and advancing AI-enabled design workflows in a fast-paced setting.

Qualifications

• PhD in a computational chemistry/biophysics/structural biology or related field, or equivalent experience.
• Experience using 3D protein structures for drug-discovery questions.
• Experience with docking, virtual screening, MD, or free-energy calculations.
• Ability to write Python scripts in a Linux/HPC environment.

Responsibilities

• Analyze protein structures and complexes to identify binding sites and allosteric opportunities.
• Integrate crystallography, cryo-EM, predicted structures, and biophysical data to guide discovery.
• Apply Schrödinger and other modeling tools to support docking, virtual screening, MD, and free-energy methods.
• Develop binding hypotheses and prioritize compounds for biochemical and cellular evaluation.
• Collaborate with medicinal chemists on binding modes, SAR, and developability.
• Incorporate AI-enabled virtual screening and property prediction into workflows.
• Coordinate with experimental teams to validate predicted mechanisms and binding sites.
• Build reproducible computational workflows with documentation of models and methods.

Skills

Python scripting

Linux HPC

Problem solving

Learning agility

Education

PhD in computational chemistry or related field

Tools

Schrödinger

Molecular modeling platforms

Linux/HPC environments

Job description

Cogent Scientific, an insourced contract research organization, is looking for the right people to accomplish our Mission: to support the life sciences industry by cultivating and empowering exceptional scientists to deliver specialized laboratory services that advance research, foster collaboration, and accelerate innovation through quality and a shared commitment to excellence. We can offer you the chance to build on your skills and knowledge while working among experts in their fields and with cutting-edge instrumentation.

Cogent Scientific offers competitive pay, attractive benefits (such as medical/dental/vision insurance; 401(k); parental leave; PTO and paid holidays; etc.) and an exciting work environment. This position may include relocation benefits as well. We aim to recruit the best people who stand out among their peers and embody our Core Values:

• Client Focused: We only succeed when our clients succeed.
• Outstanding: We deliver meticulous results through outstanding performance.
• Good: We act ethically and morally.
• Employee-Centric: We honor and support our employees.
• Nimble: We are prepared to adapt in an ever-changing industry.
• Team-Oriented: We collaborate with each other and with our clients.

We currently have a role available for a Pharma Computational Chemist.

Job duties include, but are not limited to, the following:

• Analyze protein structures and complexes to identify binding sites, interaction hotspots, cryptic or induced pockets, and allosteric opportunities.

• Integrate X-ray crystallography, cryo-EM, predicted structures, and biophysical data to guide small-molecule discovery.

• Apply Schrödinger and other molecular modeling platforms to support binding-site analysis, molecular docking, virtual screening, molecular dynamics, free-energy methods, and compound prioritization.

• Develop experimentally testable binding hypotheses and prioritize compounds for biochemical, biophysical, and cellular evaluation.

• Partner with medicinal chemists to evaluate binding modes, structure-activity relationships, physicochemical properties, synthetic feasibility, and developability.

• Apply and adapt AI-enabled virtual-screening, molecular-property prediction, and generative-design workflows.

• Collaborate with experimental scientists to design studies that validate predicted binding sites, mechanisms, and compound hypotheses.

• Integrate computational and experimental results within iterative design-make-test-analyze cycles.

• Build reproducible computational workflows and maintain clear documentation of models, assumptions, methods, and decisions.

Job requirements include, but are not limited to, the following:

• PhD in computational chemistry, computational biophysics, structural biology, medicinal chemistry, chemical biology, biochemistry, biophysics, or a related discipline, or equivalent relevant experience.

• Demonstrated experience using three-dimensional protein structures to address drug-discovery questions.

• Experience with protein-ligand interactions and one or more structure-based approaches, such as docking, virtual screening, molecular dynamics, or free-energy calculations.

• Ability to leverage internal AI-enabled drug discovery approaches via Linux/HPC environment without click interface, and write python scripts.

• Working knowledge of medicinal chemistry principles and the ability to collaborate effectively with medicinal chemists.

  Ability to integrate computational analysis with experimental data and translate results into actionable project decisions.

• Ability to work well both independently and within a team.

• Very strong problem-solving skills, a high level of learning agility, and the ability to work across functions.

• The ideal candidate should be enthusiastic and self-motivated, with the leadership and communication skills necessary to operate effectively in a fast-paced multidisciplinary environment with flexibility and an adaptable approach to goal delivery.

This is an onsite, day shift position (approx. 8a-5p local time).

Cogent Scientific provides equal employment opportunities to all applicants and does not discriminate based on any legally protected characteristic.

Additionally, if you require a reasonable accommodation during the application or interview process, please let us know.

This job posting will close by 12/31/2026 or when a candidate is identified, whichever comes first.